samtools
Verified for current stable LTS
Samtools Command: Count Alignments Per Chromosome
Use for count alignments per chromosome with Samtools. Exact CLI syntax to count alignments per chromosome using Samtools.
When to use this: Use for count alignments per chromosome with Samtools.
Command Syntax
samtools idxstats <sorted_indexed_input>samtools idxstats <sorted_indexed_input>Command Breakdown
samtools is the base executable for this command.
FAQ
Purpose: Exact syntax to count alignments per chromosome using Samtools.
Test path: Replace placeholders and run destructive commands in a disposable workspace first.
Flag behavior: Tool version, platform, and shell can change behavior.
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Related Operations
Samtools Command: Convert Sam To Bam
samtools view -S -b <input.sam> > <output.bam> Samtools Command: Index Sorted Bam samtools index <sorted_input.bam> Samtools Command: Merge Multiple Files samtools merge <output> <input1 input2 ...> Samtools Command: Print Alignment Statistics samtools flagstat <sorted_input> Samtools Command: Print Sam Header And Reads <other_command> | samtools view -h - chromosome:start-end